Genetic variation in an endemic salamander, Salamandra atra, using amplified fragment length polymorphism

Slow and steady wins the race: contrasted phylogeographic signatures in two Alpine amphibians

A deeper phylogeographic structure is expected for slow-dispersing habitat specialists compared to widespread adaptable species, especially in topographically complex regions. We tested this classic assumption by comparing the genomic (RAD-sequencing) phylogeographies of two amphibians inhabiting the Swiss Alps: the mobile, cosmopolitan common frog (Rana temporaria) against the stationary, mountain endemic Alpine salamander (Salamandra atra). Our results ran opposite of predictions: the frog displayed significantly higher genetic divergences and lower within-population variation compared to the salamander. This implies a prominent role for their distinctive glacial histories in shaping intraspecific diversity and structure: diversification and recolonization from several circum-Alpine micro-refugia for the frog versus a single refugium for the salamander, potentially combined with better population connectivity and stability. These striking differences emphasize the great variability of phylogeographic responses to the Quaternary glaciations, hence the complexity to predict general patterns of genetic diversity at the regional scale, and the forces that underlie them.

Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newt Calotriton asper (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA

Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt (Calotriton asper) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F(ST) values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper. The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.